Consistent testing for recurrent genomic aberrations

Vonn Walter, F. A. Wright, A. B. Nobel

Research output: Contribution to journalArticle

Abstract

We consider the detection and identification of recurrent departures from stationary behaviour in genomic or similarly arranged data containing measurements at an ordered set of variables. Our primary focus is on departures that occur only at a single variable, or within a small window of contiguous variables, but involve more than one sample. This encompasses the identification of aberrant markers in genome-wide measurements of DNA copy number and DNA methylation, as well as meta-analyses of genome-wide association studies. We propose and analyse a cyclic shift-based procedure for testing recurrent departures from stationarity. Our analysis establishes the consistency of cyclic shift p-values for datasets with a fixed set of samples as the number of observed variables tends to infinity, under the assumption that each sample is an independent realization of a stationary Markov chain. Our results apply to any test statistic satisfying a simple invariance condition.

Original languageEnglish (US)
Pages (from-to)783-796
Number of pages14
JournalBiometrika
Volume102
Issue number4
DOIs
StatePublished - Dec 1 2015

Fingerprint

Markov Chains
Genome-Wide Association Study
Fourier Analysis
DNA Methylation
Aberrations
Aberration
Genomics
Meta-Analysis
Genes
Genome
genomics
Testing
DNA
Invariance
Markov processes
testing
Statistics
DNA methylation
sampling
Ordered Set

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Mathematics(all)
  • Agricultural and Biological Sciences (miscellaneous)
  • Agricultural and Biological Sciences(all)
  • Statistics, Probability and Uncertainty
  • Applied Mathematics

Cite this

Walter, Vonn ; Wright, F. A. ; Nobel, A. B. / Consistent testing for recurrent genomic aberrations. In: Biometrika. 2015 ; Vol. 102, No. 4. pp. 783-796.
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Consistent testing for recurrent genomic aberrations. / Walter, Vonn; Wright, F. A.; Nobel, A. B.

In: Biometrika, Vol. 102, No. 4, 01.12.2015, p. 783-796.

Research output: Contribution to journalArticle

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